EP0978570B1 - Detecting mycobacterium tuberculosis by nucleic acid sequence amplification - Google Patents

Detecting mycobacterium tuberculosis by nucleic acid sequence amplification Download PDF

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EP0978570B1
EP0978570B1 EP99121906A EP99121906A EP0978570B1 EP 0978570 B1 EP0978570 B1 EP 0978570B1 EP 99121906 A EP99121906 A EP 99121906A EP 99121906 A EP99121906 A EP 99121906A EP 0978570 B1 EP0978570 B1 EP 0978570B1
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sequence
nucleic acid
oligonucleotide
promoter
primer
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EP0978570A2 (en
EP0978570A3 (en
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Diane L. Mcallister
Philip W. Hammond
Y. Yang Yeasing
Sherrol Mcdonough
Daniel Kacian
Nanibhushan Dattagupta
Thomas B. Ryder
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Gen Probe Inc
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Gen Probe Inc
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6848—Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/35—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Mycobacteriaceae (F)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6865—Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • C12Q1/702—Specific hybridization probes for retroviruses
    • C12Q1/703—Viruses associated with AIDS

Definitions

  • This invention relates to methods for increasing the number of copies of a specific nucleic acid sequence or "target sequence" of M. tuberculosis rRNA which may be present either alone or as a component, large or small, of a homogeneous or hetero-geneous mixture of nucleic acids.
  • the mixture of nucleic acids may be that found in a sample taken for diagnostic testing, environmental testing, for research studies, for the preparation of reagents or materials, for other processes such as cloning, or for other purposes.
  • the selective amplification of specific nucleic acid sequences is of value in increasing the sensitivity of diagnostic and environmental assays while maintaining specificity; increasing the sensitivity, convenience, accuracy and reliability of a variety of research procedures; and providing ample supplies of specific oligonucleotides for various purposes.
  • the present invention is particularly suitable for application to diagnostic testing due to the convenience with which it may be practised.
  • the detection and/or quantitation of specific nucleic acid sequences is an increasingly important technique for identifying and classifying microorganisms, diagnosing infectious diseases, detecting and characterizing genetic abnormalities, identifying genetic changes associated with cancer, studying genetic susceptibility to disease, and measuring response to various types of treatment.
  • Such procedures have also found expanding uses in detecting and quantitating microorganisms in foodstuffs, environmental samples, seed stocks, and other types of material where the presence of specific microorganisms may need to be monitored.
  • a common method for detecting and quantitating specific nucleic acid sequences is nucleic acid hybridization. This method is based on the ability of two nucleic acid strands that contain complementary or essentially complementary sequences to specifically associate, under appropriate conditions, to form a double-stranded structure.
  • a specific nucleic acid sequence known as the "target sequence”
  • a labelled oligonucleotide known as a "probe”
  • the probe is mixed with a sample suspected of containing the target sequence, and conditions suitable for hybrid formation are created.
  • the probe hybridizes to the target sequence if it is present in the sample.
  • the probe-target hybrids are then separated from the single-stranded probe in one of a variety of ways.
  • the amount of label associated with the hybrids is then measured as an indication of the amount of target sequence in the sample.
  • nucleic acid hybridization assays The sensitivity of nucleic acid hybridization assays is limited primarily by the specific activity of the probe, the rate and extent of the hybridization reaction, the performance of the method for separating hybridized and unhybridized probe, and the sensitivity with which the label can be detected.
  • the most sensitive procedures may lack many of the features required for routine clinical and environmental testing such as speed, convenience, and economy. Furthermore, their sensitivities may not be sufficient for many desired applications.
  • PCR polymerase chain reaction
  • the primers are complementary to the 3'-end portion of the target sequence or its complement and must complex with those sites in order for nucleic acid synthesis to begin.
  • the strands are separated, generally by thermal denaturation, before the next synthesis step.
  • copies of both strands of a complementary sequence are synthesized.
  • the strand separation step used in PCR to separate the newly synthesized strands at the conclusion of each cycle of the FCR reaction is often thermal denaturation.
  • a thermostable enzyme is required or new enzyme must be added between thermal denaturation steps and the initiation of the next cycle of DNA synthesis.
  • the requirement of repeated cycling of reaction temperature between several different and extreme temperatures is a disadvantage of the PCR procedure.
  • programmable thermal cycling instruments are required.
  • the PCR procedure has been coupled to RNA transcription by incorporating a promoter sequence into one of the primers used in the PCR reaction and then, after amplification by the PCR procedure for several cycles, using the double-stranded DNA as template for the transcription of single-stranded RNA.
  • a promoter sequence into one of the primers used in the PCR reaction
  • the double-stranded DNA as template for the transcription of single-stranded RNA.
  • TAS transcription amplification system
  • 0300796 (Becker et al.) describes an amplification method in which a primer is hybridized to the target sequence and the resulting duplex is cleaved prior to the extension reaction and amplification; in the case where the primer extends past the region of hybridization, it requires cleavage prior to the extension and the primer must be blocked at its 3'-end to prevent any unwanted extension reactions from occurring prior to amplification.
  • Urdea WO 91/10746, describes a signal amplification method that incorporates a T7 promoter sequence.
  • LCR ligase chain reaction
  • Another method is that described in EP-A-0 427 073 published May 15, 1991 in which a palindromic probe able to form a hairpin and having a functional promoter region in the hairpin is hybridized to a target sequence, then ligated to another oligonucleotide hybridized to the target sequence such that specific RNA transcripts may be made.
  • RNAs may be made using a recombinant single-stranded RNA molecule having a recognition sequence for the binding of an RNA-directed polymerase, preferably C ⁇ replicase.
  • an RNA-directed polymerase preferably C ⁇ replicase.
  • a number of steps are required to insert the specific sequence into a DNA copy of the variant molecule, clone it into an expression vector, transcribe it into RNA and then replicate it with Q ⁇ replicase.
  • Nucleic acid means either RNA or DNA, along with any nucleotide analogues or other molecules that may be present in the sequence and that do not prevent performance of the present invention.
  • a "template” is a nucleic acid molecule that is able to be copied by a nucleic acid polymerase.
  • a template may be either RNA or DNA, and may be any of single-stranded, double-stranded or partially double-stranded, depending on the polymerase.
  • the synthesized copy is complementary to the template.
  • copies also includes nucleic acid having the equivalent RNA or DNA sequence to a template, which are commonly referred to as homologous sequences in the art.
  • a “primer” is an oligonucleotide that is complementary to a template that hybridizes with the template to give a primer/template complex for initiation of synthesis by a DNA polymerase, such as a reverse transcriptase, and which is extended by the addition of covalently bonded bases linked to its 3' end that are complementary to the template.
  • a DNA polymerase such as a reverse transcriptase
  • the result is a primer extension product.
  • Virtually all DNA polymerases (including reverse transcriptases) that are known require complexing of an oligonucleotide to a single-stranded template ("priming") to initiate DNA synthesis.
  • a primer may be a part of a promoter-primer. Such primers are generally between 10 and 100 bases in length, preferably between 20 and 50 bases in length.
  • a “promoter” or “promoter sequence” is a specific nucleic acid sequence that is recognized by a DNA-dependent RNA polymerase ("transcriptase”) as a signal to bind to a nucleic acid molecule and begin the transcription of RNA at a specific site.
  • transcriptionases DNA-dependent RNA polymerase
  • Such transcriptases generally require that the promoter and its complement be double-stranded; the template portion need not be double-stranded.
  • Individual DNA-dependent RNA polymerases recognize a variety of different promoter sequences that can vary markedly in their efficiency of promoting transcription. When an RNA polymerase binds to a promoter sequence to initiate transcription, that promoter sequence is not part of the sequence transcribed. Thus, the RNA transcripts produced thereby will not include the promoter sequence.
  • a promoter-primer comprises a promoter and a primer. It is an oligonucleotide that is sufficiently complementary to the 3'-end of a target nucleic acid sequence to complex at or near the 3'-end of that target nucleic acid sequence, which means that the promoter-primer complexes near enough the end of the target sequence to allow amplification of enough of the target sequence that the requirements of the assay, testing, cloning or other use for the amplified nucleic acid are met.
  • the promoter-primer is used as a template to create a complementary nucleic acid sequence extending from the 3'-end (also known as the 3' terminus) of a target nucleic acid sequence, to result in a generally double stranded promoter, subject to any denaturing or enzymatic activity that may disrupt the double strand.
  • Such promoter-primers are generally between 40 and 100 bases in length, preferably between 40 and 60 bases.
  • a DNA- or RNA-dependent DNA polymerase also creates a complementary strand to the target nucleic acid molecule, using the target sequence as a template.
  • the 3'-end of the primer or promoter-primer may be modified, or blocked, so as to prevent or reduce the rate and/or extent of an extension reaction from proceeding therefrom.
  • a primer or promoter-primer having both modified and unmodified members consists of essentially the same nucleic acid sequence for the purposes of the present invention.
  • the modified primer or promoter-primer does not contain a different complexing sequence (primer) in that both the modified and unmodified oligonucleotide hybridize in effectively the same position (plus or minus about ten bases) on the target nucleic acid sequence.
  • the modified promoter-primer does not contain a different recognition sequence (promoter) from the unmodified promoter-primer.
  • the modified and unmodified primers or promoter-primers are the same, are recognized by the same RNA polymerase, and hybridize to more or less the same target sequence (although not necessarily at precisely the same position).
  • the modified and unmodified primers or promoter-primers are identical except for the modification.
  • the 3'-end of the target complementary portion of a primer or promoter-primer can be modified in a variety of ways well known to those skilled in the art.
  • Appropriate modifications to a promoter-primer can include addition of ribonucleotides, 3' deoxynucleotide residues, ( e.g. , cordycepin (CO, Glen Research)), 3',2'-dideoxy nucleotide residues, modified nucleotides with nonphosphodiester backbone linkages (such as phosphorothioates), and non-nucleotide linkages such as described in Arnold, et al., WO 89/02439 (RS) or alkane-diol modifications (Wilk et al.
  • RP Nuc. Acids Res. 18:2065, 1990) (RP), or the modification may simply consist of one or more nucleotide residues 3' to the hybridizing sequence that are uncomple-mentary to the target nucleic acid.
  • RP Nuc. Acids Res. 18:2065, 1990
  • a mixture of modified and unmodified oligonucleotides may be used in an amplification reaction, and a broad range of ratios of modified to unmodified oligonucleotide (e.g., from 1:1 to 1,000:1) can be used.
  • a mixture of oligonucleotides with different 3' modifications may also be used.
  • nucleic acid synthesis is greatly simplified and clarified by adopting terms to name the two complementary strands of a nucleic acid duplex.
  • the strand encoding the sequences used to produce proteins or structural RNAs was designated as the "plus” strand and its complement the “minus” strand. It is now known that in many cases, both strands are functional, and the assignment of the designation "plus” to one and “minus”to the other must then be arbitrary. Nevertheless, the terms are very useful for designating the sequence orientation of nucleic acids and will be employed herein for that purpose, with the "plus” strand denominating the original target sequence strand that is complexed with the first primer or promoter-primer.
  • target nucleic acid sequence has a desired nucleic acid sequence to be amplified, and may be either single-stranded or double-stranded and may include other sequences 5' or 3' of the sequences to be amplified which may or may not be amplified.
  • the target nucleic acid sequence includes the complexing sequences to which the promoter-primer hybridizes during performance of the present invention.
  • the term refers to either the (+) or (-) strand, and will also refer to the sequence complementary to the target sequence .
  • the target nucleic acid sequence is originally double-stranded, the term refers to both the (+) and (-) strands.
  • a "DNA-dependent DNA polymerase” is an enzyme that synthesizes a complementary DNA copy from a DNA template.
  • An example is bacteriophage T7 DNA polymerase. All known DNA-dependent DNA polymerases require a complementary primer, which can be RNA or DNA, or a copolymer, to initiate synthesis. It is known that under suitable conditions certain DNA-dependent DNA polymerases may synthesize a complementary DNA copy from an RNA template.
  • a "DNA-dependent RNA polymerase” or “transcriptase” is an enzyme that synthesizes multiple RNA copies from a double-stranded or partially-double stranded DNA molecule having a (usually double-stranded) promoter sequence. It should be noted that the present invention includes single stranded promoter sequences in the promoter-primer, along with the RNA polymerases that recognize them. The RNA molecules ("transcripts”) are synthesized in the 5' ⁇ 3' direction of the RNA molecule, beginning at a specific position just downstream of the promoter. Examples of transcriptases are the DNA-dependent RNA polymerases from bacteriophages T7, T3, and SP6.
  • RNA-dependent DNA polymerase or "reverse transcriptase” is an enzyme that synthesizes a complementary DNA copy from an RNA template. All known reverse transcriptases also have the ability to make a complementary DNA copy from a DNA template; thus, they are both RNA- and DNA-dependent DNA polymerases. A primer is required to initiate synthesis with either the RNA or DNA templates.
  • RNAse H is an enzyme that degrades the RNA portion of an RNA:DNA duplex.
  • RNAse H's may be endo-nucleases or exonucleases.
  • Avian myeloblastosis virus and Moloney murine leukemia virus reverse transcriptases contain an RNAse H activity in addition to their polymerase activity. Some cloned reverse transcriptases lack RNAse H activity.
  • hybridize and “complex” refer to the formation of duplexes between nucleotide sequences that are sufficiently complementary to form duplexes (or “complexes”) via Watson-Crick base pairing.
  • a promoter-primer or primer “hybridizes” with target (template)
  • such complexes or hybrids are sufficiently stable to serve the priming function required by a DNA polymerase to initiate DNA synthesis.
  • Specificity is a characteristic of a nucleic acid sequence that describes its ability to distinguish between target and non-target sequences, dependent on sequence and assay conditions.
  • the present invention provides a kit containing a first oligonucleotide consisting of the sequence xGCCGTCACCCCACCAACAAGCT (SEQ ID No. 22), and a second oligonucleotide consisting of the sequence
  • xGGGATAAGCCTGGGAAACTGGGTCTAATACC SEQ ID No. 2
  • x is nothing or is a sequence recognized by an RNA polymerase.
  • Such a kit may be employed to carry out an auto-catalytic method of synthesizing multiple copies of the target M. tuberculosis rRNA nucleic acid sequence (i.e. , the method cycles automatically without the need to modify reaction condi-tions such as temperature, pH, or ionic strength).
  • Such a method features treating a target sequence with a first oligonucleotide (that has a complex-ing sequence sufficiently complementary to a 3'-end portion of the target sequence to hybridize therewith (this alone is termed a primer), and that has a sequence 5' to the complexing sequence that includes a sequence which, in double-stranded form, acts as a promoter for an RNA polymerase (this arrangement is termed a promoter-primer)), and a second oligonucleotide (which is a primer or promoter-primer that has a complexing sequence sufficiently complementary to the complement of the target sequence to hybridize therewith), under conditions in which an oligonucleotide/target sequence complex may be formed and DNA and RNA synthesis may occur.
  • a first oligonucleotide that has a complex-ing sequence sufficiently complementary to a 3'-end portion of the target sequence to hybridize therewith
  • a primer that has a sequence 5' to the complexing sequence that includes a sequence
  • one or both of the first and second oligonucleotides is a mixture of a blocked and an unblocked oligonucleotide sequence (blocked oligonucleotides have a modified 3' end to prevent or reduce the rate and/or extent of primer extension by a DNA polymerase), or a mixture of oligonucleotides with different 3' modifications.
  • Such a mixture significantly enhances the efficiency of the specific amplification reaction compared to use of only blocked or only unblocked oligonucleotides.
  • the ratio of such oligonucleotides can be varied dependent upon the specific template sequence to be amplified, but generally is between 1:1 and 1000:1 blocked to unblocked. There is no requirement that the target sequence have defined 3'- or 5'- ends.
  • an amplification method as described above may include (a) treating a target sequence with a first promoter-primer oligonucleo-tide that has a complexing sequence sufficiently complementary to a 3'-end portion of the target sequence to hybridize therewith, and that has a sequence 5' to the complexing sequence that includes a sequence which, in double- stranded form, acts as a promoter for an RNA poly-merase, under conditions in which an oligonucleotide/ target sequence complex may be formed and DNA synthesis may be initiated by an appropriate polymerase (e.g.
  • a DNA polymerase incubating the first oligonucleotide/ target complex under extension reaction conditions so that the 3'-end of the target may be extended to produce a hybrid template for an RNA polymerase; and (c) incubating the hybrid template under conditions in which multiple RNA copies of the target sequence may be produced using an RNA polymerase that recognizes the promoter sequence.
  • the invention also includes generation of a 3'-end of an RNA target sequence in step (b) by the action of an enzyme that selectively degrades the RNA portion of an RNA:DNA hybrid (e.g., RNase H). The RNA so produced may autocata-lytically cycle to produce more product.
  • the following steps occur: (a) contacting a nucleic acid (e.g. , RNA or DNA) target sequence with a first oligonucleotide primer or promoter-primer under conditions in which a first oligonucleotide/target sequence complex is formed such that DNA synthesis may be initiated by an appropriate polymerase (e.g.
  • a DNA poly-merase incubating the first oligonucleotide under extension reaction conditions so that the target may be used by the polymerase as a template to give a first DNA extension product complementary to the target (if the first primer is not blocked); (c) if the target is an RNA molecule, separating the DNA extension product from the RNA target using an enzyme that selectively degrades the RNA target, or if the target is a DNA molecule, separating the two DNA strands (e.g.
  • the second oligonucleotide is a promoter-primer, which means the second oligonucleotide has a sequence 5' to the complexing sequence that includes a promoter sequence for an RNA polymerase.
  • the first and/or second oligonucleotides consist of either a mixture of a blocked and an unblocked oligonucleotide, or a mixture of oligonucleotides with different 3' modifications.
  • the amplification reaction is performed in a mixture consisting essentially of the necessary reactants and reagents.
  • a mixture may also contain enzymes or other substituents that do not qualitatively affect the amplification of the invention (e.g., the mechanism of the reaction).
  • substituents may affect the amount of amplification observed.
  • the mixture may contain other promoter-primers for the same target sequence, or may contain "helper" oligonucleotides.
  • helper oligonucleotides are used in a manner similar to the hybridization helper probes described by Hogan et al., U.S. Patent 5,030,557
  • helper oligonucleotides could be used in an amplification protocol without adverse effect on the efficiency of the procedure.
  • the first oligonucleotide may be a promoter-primer and the second oligonucleotide may be a primer, or vice versa , or both the first and second oligonucleotides may be promoter-primers, with either identical promoters (in the sense that the promoters are recognized by the same RNA polymerase) or different promoters. Use of different promoters is particularly useful when the amplified nucleic acid will be used for cloning.
  • the first and second oligonucleotides and the RNA produced from the target sequence may then be used to autocatalytically synthesize multiple copies (by which is meant both complementary and homologous nucleic acid sequences) of the target sequence.
  • the modified primer or promoter-primer of a kit of the invention consists essentially of a single nucleic acid sequence that has a modification at or near (within 3 bases) the 3'-end of the given primer or promoter- primer that alters (decreases or blocks) extension of the primer on a template by a DNA polymerase.
  • this modified primer or promoter-primer is mixed with an unmodified primer or promoter-primer consisting essentially of the same nucleic acid sequence, along with one or more other primers or promoter-primers of a different nucleic acid sequence (that may also be a mixture of blocked and unblocked oligonucleotides).
  • Kits of the invention may also include mixtures of primers and promoter-primers with more than one modification at or near their 3'-ends.
  • a kit of the invention may be employed after generation of a defined 5' end (i.e., one of known sequence) in an RNA target sequence by treating the RNA with a DNA oligonucleotide which hybridizes near the second primer binding site and thereby forms a substrate for RNAse H. This substrate is then cleaved by RNAse H to define the 5' end of the RNA target, which can be amplified as discussed above.
  • Amplification employing a kit of the invention may involve cooperative action of a DNA polymerase (such as a reverse transcriptase) and a DNA-dependent RNA polymerase (tran-scriptase) with an enzymatic hybrid-separation step to produce products that may themselves be used to produce additional product, thus resulting in an autocatalytic reaction without requiring manipulation of reaction conditions, such as in thermal cycling. Further, in some embodiments of the present invention that include a preliminary procedure, all but the initial step(s) of the preliminary procedure are carried out at one temperature.
  • a DNA polymerase such as a reverse transcriptase
  • tran-scriptase DNA-dependent RNA polymerase
  • a sample including rRNA target to be amplified is mixed with a buffer concentrate containing the buffer, salts (e.g., divalent cations such as magnesium), nucleotide triphosphates, primers and/or promoter-primers (blocked and/or unblocked), a thiol reducing agent such as dithiothreitol, and a polycation such as spermidine.
  • salts e.g., divalent cations such as magnesium
  • nucleotide triphosphates e.g., primers and/or promoter-primers (blocked and/or unblocked)
  • a thiol reducing agent such as dithiothreitol
  • a polycation such as spermidine
  • kits of the invention may be used in many other assay systems known to those skilled in the art.
  • Yet another aspect of the invention features a mixture of modified and unmodified oligonucleotides or a mixture of differently modified oligonucleotides, said mixture being a mixture of primers or a mixture of promoter-primers having the same promoter sequence and wherein each modified or unmodified oligonucleotide hybridizes to essentially the same target sequence and wherein said oligonucleotides are selected from oligonuleotides according to any one of (a) to (c) below:
  • Kits of the invention may be diagnostic kits or other kits for use in diagnostic procedures, or other procedures, and the invention is adaptable to multi-well technology which may be provided in kit format.
  • a kit of the invention may advantageously provide oligonucleotides for an amplification method that synthesizes RNA copies of an M. tuberculosis rRNA target sequence by use of a mixture of blocked and unblocked promoter-primers, or promoter- primers with different 3' modifications, consisting essentially of the same nucleic acid sequence in a ratio that provides for lessened non-specific by-products.
  • the amplification process occurs spontaneously and isothermally under a broad range of conditions.
  • the amplification reactions described below are a series of logical steps. The relative rate of each step will determine the effective yield of amplification product.
  • Use of a mixture of blocked and unblocked primers reduces the side reactions, and hence improves amplification. Side products, such as "primer-dimers" have been described, and are well known in the art to affect the efficiency of amplification reactions.
  • An amplification process as presented herein reduces the efficiency of formation of such byproducts, therefore enhancing a
  • Suitable DNA polymerases include reverse transcriptases such as avian myeloblas-tosis virus (AMV) reverse transcriptase and Moloney murine leukemia virus (MMLV) reverse transcriptase.
  • Promoters or promoter sequences suitable for incorporation in promoter-primers used in the present invention are nucleic acid sequences (either naturally occurring, produced synthetically or by a restriction endonuclease digest) that are specifically recognized by an RNA polymerase that recog-nizes and binds to that sequence and initiates the process of transcription whereby RNA transcripts are produced.
  • Promoter sequences for which there is a known and available polymerase that is capable of recognizing the initiation sequence are particularly suitable to be employed.
  • Such promoters include those that are recognized by certain bacteriophage polymerases such as those from bacteriophage T3, T7 or SP6.
  • the sequence may optionally include nucleotide bases extending beyond the actual recognition site for the RNA polymerase that may impart added stability or susceptibility to degradation processes or increased transcription efficiency.
  • RNAse H activity of AMV or MMLV reverse transcriptase
  • exogenous RNAse H such as E . coli RNAse H
  • the examples show that the addition of exogenous RNAse H is not required, the RNAse H activity present in AMV reverse transcriptase may be inhibited by relatively large amounts of heterologous DNA present in the reaction mixture; one solution to the problem is to add exogenous RNAse H.
  • Another instance when added RNAse H may be required is when an oligonucleo-tide hybridizes internally ( i.e. , the oligonucleotide hybridizes such that target sequence nucleotides extend past both the 3' and 5' ends of the oligonucleotide) on the target RNA.
  • the second oligonucleotide providing a primer sequence may be blocked or modified similarly to the first oligonucleotide.
  • the second oligonucleotide is modified.
  • the first oligonucleotide is not a promoter-primer
  • the second oligonucleotide is a promoter-primer.
  • the first oligonucleotide is only a primer, then it may be unblocked, and the second oligonucleotide is then a promoter-primer including both blocked and unblocked constituents consisting essentially of a single nucleic acid sequence.
  • RNA copies or transcripts produced may autocatalytically multiply without further manipulation.
  • the first and second oligonucleotides are both promoter-primers, and either or both may each consist of both modified and unmodified promoter-primers.
  • both promoters are recognized by the same RNA polymerase unless it is intended to introduce the second promoter for purposes other than amplification, such as cloning.
  • transcripts complementary to both strands of the double-stranded template will be produced during the autocatalytic reaction and the number of copies of the target sequence synthesized may be enhanced.
  • the second oligonucleotide (primer or promoter-primer) now defines the other end; the termini may also be defined by a specific restriction endonuclease, or by other suitable means (which may include a natural 3'-end).
  • the RNA transcripts may have different termini from the original target nucleic acid, but the sequence between the first oligonucleotide and the second oligonucleotide remains intact. The RNA transcripts so produced may automatically recycle in the above system without further manipulation. Thus, this reaction is autocatalytic.
  • either oligonucleotide may have nucleotide sequences 5' to its priming sequence that can result in the addition of extra nucleotide sequence to the eventually resulting double stranded DNA; the extra nucleotide sequence is not limited to a promoter sequence.
  • the present invention may consist of a first and second oligonucleotide in which a promoter-primer is provided which consists only of a blocked oligonucleotide, or only of an unblocked oligonucleotide, or an oligonucleotide with a mixture of different modifications at or near the 3'-end.
  • Amplification may be performed in the presence of additives to enhance amplification.
  • additives such as dimethyl sulfoxide, dimethyl formamide, ethylene glycol, glycerol or zinc have been used.
  • the components of the reaction mixture may be added stepwise or at once.
  • the reaction advantageously takes place under conditions suitable for maintaining the stability of reaction components, such as the component enzymes, and without requiring modification or manipulation of reaction conditions during the course of the amplification reaction.
  • kits of the present invention demonstrate the utility of kits of the present invention. They are not limiting and should not be considered as such.
  • reaction conditions for amplification were 50 mM Tris-HCl, 35 mM KCl, 20 mM MgCl 2 , 15 mM N-acetylcysteine, 4 mM rATP, 4 mM rCTP,4 mM rGTP, 4 mM rUTP, 1 mM dATP, 1 mM dCTP, 1 mM dGTP, 1 mM dTTP, 10% glycerol, 10% dimethyl sulfoxide, 300-600 units MMLV reverse transcriptase, 200-400 units T7 RNA polymerase, 0.15 ⁇ M each primer or promoter-primer, and specified amounts of template and enzymes in 100 ⁇ l volumes at 42°C for one hour. Dithiothreitol, spermidine and/or polyethyleneimine (PEI) may also advantageously be added to the reaction mixture.
  • PEI polyethyleneimine
  • RNA polymerase T7 or T3 RNA polymerase and Moloney murine leukemia virus (MMLV) reverse transcriptase.
  • MMLV Moloney murine leukemia virus
  • Other RNA polymerases with different promoter specificities are also suitable.
  • the relative amplification was measured as follows. A sample of the amplification reaction mixture (usually 10 ⁇ l) was added to 100 ⁇ l of a luminescently labelled probe (for example, labelled with an acridinium ester - see HPA reference above) solution containing approximately 75 fmol probe, 0.1 M lithium succinate, pH 4.7, 2% (w/v) lithium lauryl sulfate, 15 mM aldrithiol, 20 mM EDTA, and 20 mM EGTA, and mixed. The reactions were then incubated 20 minutes at 60°C and cooled. To each hybridization reaction was added 300 ⁇ l of 0.6 M sodium borate pH 8.5, 1% TritonJx-100.
  • a luminescently labelled probe for example, labelled with an acridinium ester - see HPA reference above
  • the reactions were then mixed and incubated six minutes at 60°C to destroy the chemiluminescent label of the unhybridized probe.
  • This method of destruction of the chemiluminescent label of unhybridized probe is quite specific; only a very small fraction of the unhybridized probe remains chemiluminescent.
  • the reactions were cooled and the remaining chemiluminescence was quantified in a luminometer upon the addition of 200 ⁇ l 0.1% hydrogen peroxide, 1 mM nitric acid, and surfactant, and 200 ⁇ l 1.0 N sodium hydroxide. In the assay, hybridized probe emits light.
  • the quantity of photons emitted are measured in a luminometer and the results are reported as Relative Light Units or RLU. Since the reaction that destroys the chemiluminescent label of unhybridized probe is not 100% effective, there is generally a background level of signal present in the range of about 1000 to 2000 RLU.
  • assays employing hybridization to isotopically labeled probes, blotting techniques and electrophoresis. These reaction conditions are not necessarily optimized, and have been changed as noted for some systems.
  • the oligonucleotide sequences used are exemplary and are not meant to be limiting as other sequences have been employed for these and other target sequences.
  • a promoter-primer complementary to a sequence within M. tuberculosis rRNA (Seq ID No. 1; primer portion is SEQ ID No. 22) was synthesized either unmodified or with a 3' alkane diol (RP) or 3' cordycepin (CO) and incubated with a primer of the same sense as the target RNA (Seq ID No. 2) and 3 zmol of target under the conditions described above.
  • the reac-tions were analyzed with a probe of the same sense as the target RNA (Seq ID No.
  • helper oligonucleotides as described in Hogan (U.S. Patent 5,030,557, Means for Enhancing Nucleic Acid Hybridization, Seq ID Nos. 4 and 5).
  • the results show that significant amplification does occur with a promoter-primer containing a 3' modification.
  • Promoter-primer modification RLU Unmodified 314,445 3'cordycepin 71,382 Unmodified 683,737 3'-RP 70,014
  • a mixture of modified and unmodified primers and promoter-primers were used to amplify 3 zmol M . tuberculosis rRNA.
  • a mixture of 2 pmol RP-modified promoter-primer and 13 pmol of CO-modified promoter-primer were incubated with unmodified primer or a mixture of unmodified primer and primer synthesized with a 3' phosphorothioate nucleotide (PS).
  • PS 3' phosphorothioate nucleotide
  • the sequences and hybridization probes are as in Example 1.
  • Primer modification RLU Unmodified PS modified -- 15 pmol 118,411 1 pmol 14 pmol 364,733 No target 1,266 Under these conditions, the mixture of modified and unmodified primers work best.

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